/usr/include/relion-1.4/src/ctffind_runner.h is in librelion-dev-common 1.4+dfsg-3ubuntu1.
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*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* This complete copyright notice must be included in any revised version of the
* source code. Additional authorship citations may be added, but existing
* author citations must be preserved.
***************************************************************************/
#ifndef CTFFIND_RUNNER_H_
#define CTFFIND_RUNNER_H_
#include <glob.h>
#include <vector>
#include <string>
#include <stdlib.h>
#include <stdio.h>
#include "src/metadata_table.h"
#include "src/image.h"
#include <src/time.h>
class CtffindRunner
{
public:
// I/O Parser
IOParser parser;
// Verbosity
int verb;
// Output rootname
FileName fn_in, fn_out;
// Filenames of all the micrographs to estimate the CTF from
std::vector<FileName> fn_micrographs;
// Dimension of squared area of the micrograph to use for CTF estimation
int ctf_win;
// CTFFIND executable
FileName fn_ctffind_exe;
// Continue an old run: only estimate CTF if logfile WITH Final Values line does not yet exist, otherwise skip the micrograph
bool continue_old;
////// CTFFIND parameters
// Size of the box to calculate FFTw
DOUBLE box_size;
// Minimum and maximum resolution (in A) to be taken into account
DOUBLE resol_min, resol_max;
// Defocus search parameters (in A, positive is underfocus)
DOUBLE min_defocus, max_defocus, step_defocus;
// Amount of astigmatism (in A)
DOUBLE amount_astigmatism;
// Voltage (kV)
DOUBLE Voltage;
// Spherical aberration
DOUBLE Cs;
// Amplitude contrast (e.g. 0.07)
DOUBLE AmplitudeConstrast;
// Magnification
DOUBLE Magnification;
// Detector pixel size (um)
DOUBLE PixelSize;
// Flag to only join results into a star file
bool do_only_join_results;
public:
// Read command line arguments
void read(int argc, char **argv, int rank = 0);
// Print usage instructions
void usage();
// Initialise some stuff after reading
void initialise();
// Execute all CTFFIND jobs to get CTF parameters
void run();
// Harvest all CTFFIND results into a single STAR file
void joinCtffindResults();
// Execute CTFFIND for a single micrograph
void executeCtffind(FileName fn_mic);
};
// Get micrograph metadata
bool getCtffindResults(FileName fn_mic, DOUBLE &defU, DOUBLE &defV, DOUBLE &defAng, DOUBLE &CC,
DOUBLE &HT, DOUBLE &CS, DOUBLE &AmpCnst, DOUBLE &XMAG, DOUBLE &DStep, bool die_if_not_found = true);
#endif /* CTFFIND_RUNNER_H_ */
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